Defense attorneys obtained internal emails that show the commandant and his civilian legal adviser, Robert Hogue, stayed involved. For example, Gen. Amos expressed displeasure in an email to Gen. Waldhauser’s successor on how he was handling the cases.

Asked on NPR whether he fired Gen. Waldhauser because he balked, Gen. Amos said, “I think that’s absolutely specious. I think that — and I’ve kept my mouth shut for a year and a half — and I think that’s absolutely specious. I mean, I can’t speak for him, but I can speak for myself.”

A spokesman for Gen. Waldhauser said he “does not have anything more to add on this issue.”

Another top Marine has split with headquarters over how it treated Capt. Clements.

Gen. John Kelly, a four-star officer who heads U.S. Southern Command, came forward to criticize the prosecution of Capt. Clement, and thus Gen. Amos, who publicly called for punishing those linked to the urination incident.

Gen. Kelly testified on Capt. Clement’s behalf at the board of inquiry last fall. He praised him as an officer and said he was being treated unfairly.

“I can’t offer an official apology to him and his family, but I think at the end of this board, he should receive that from someone,” Gen. Kelly testified, according to the Marine Corps Times.

The Marine Corps Times, which has reported extensively on the Clement case and Gen. Amos‘ involvement, found its copies banished from the front of military-run stores. The order came from Marine headquarters, the independent newspaper said.

Capt. Clement was charged with dereliction of duty for not better supervising the snipers. He had no knowledge of the urination incident.

The Corps punished eight Marines tied to the urination or the unit. The four enlisted Marines shown in the video pleaded guilty and were reduced in rank.

One scout-sniper, a staff sergeant, said a fellow Marine was killed that day by an improvised explosive device and they believe the Taliban they killed were responsible.

Defending the commandant

Still pending is the whistleblower case of Maj. James Weirick, a staff attorney at the Marine Corps Base at Quantico, Va. He informed defense attorneys about what he considered illegal command influence by Gen. Amos and his staff and filed complaints with the Pentagon inspector general.

After Maj. Weirick wrote an email to a potential witness urging him to tell the truth, Gen. Amos‘ staff had Maj. Weirick removed from his legal duties and ordered him to undergo a mental health exam, which he passed. Mr. Hogue said he feared Maj. Weirick might become another mass killer like Washington Navy Yard shooter Aaron Alexis.

The inspector general now is investigating whether Maj. Weirick is the victim of whistleblower retaliation. He has a strong ally in Rep. Walter B. Jones, North Carolina Republican, who personally attacked the commandant last week when he appeared before the House Committee on Armed Services on the 2015 budget.